mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-26 04:09:39 +03:00
* Fix MPI Fortran configuration for HDF5Examples (#6206) When building Fortran parallel examples without MPI wrappers, the compiler couldn't find mpi.mod because MPI_Fortran_INCLUDE_DIRS was not populated. This occurred because find_package(MPI) was only called for C, not Fortran. Added enable_language(Fortran) and find_package(MPI REQUIRED COMPONENTS Fortran) to properly configure MPI for Fortran examples, ensuring MPI include directories and libraries are correctly set. * Adds RFCs to the RFC table (#6190) * Added two RFCs to the RFC table "Adding support for digitally signed plugins to HDF5" " Write-Ahead log" * Updated to use the ACM link * Add HDF5 2.0.0 Library Migration Guide (#6183) * Add HDF5 2.0.0 Library Migration Guide * Revise HDF5 migration guide for version 2.0.0 Use 2.0.0 consistently. * Clarify API changes in HDF5 2.0.0 Migration Guide * Fixes the "multiple @param documentation sections" doxygen warnings (#6195) Addresses the "multiple @ param documentation sections" warnings are caused by the interaction of three things: 1. MACRO_EXPANSION = YES with EXPAND_ONLY_PREDEF = NO in Doxyfile.in 2. Versioned API macros in H5version.h like: \def documentation in APIVersions.dox like: 3. \def H5Tarray_create \api_vers_2{H5Tarray_create,H5Tarray_create1,H5Tarray_create2} Because Doxygen expands all macros, it sees H5Tarray_create as an alias for H5Tarray_create1. It then associates documentation from both the \def block (for the macro) and the function's own doc block (with \param entries) with the same function — resulting in "multiple @ param documentation sections." * Update Doxygen version from 1.16.0 to 1.16.1 Use Doxygen 1.16.1 for all platforms. This version includes the latest bug fixes and improvements while maintaining compatibility with our documentation format. * Fix Windows Doxygen installation for version 1.16.1 Handle different Windows binary naming conventions across Doxygen versions: - 1.16.1 uses: doxygen-VERSION.windows.x64.bin.zip - 1.16.0 uses: doxygen-VERSION.x64.bin.zip Try the newer naming convention first, then fall back to the older one if the download fails. This ensures compatibility across versions. * Use ssciwr/doxygen-install in setup-doxygen action Replace direct installation of official Doxygen binaries with ssciwr/doxygen-install action. This avoids Java documentation parsing errors that occur with official binaries but not with distribution builds. The setup-doxygen action now serves as a thin wrapper around ssciwr/doxygen-install@f13be16c83 (v1), using commit hash for security and reproducibility. * Remove redundant version specification from workflows The setup-doxygen action already has a default version (1.16.1), so explicit version specification in workflows is unnecessary. This follows DRY principles and makes version updates simpler. * Updates to #6205 (#6208) * Fix MPI Fortran configuration for HDF5Examples (#6205) When building Fortran parallel examples standalone without MPI wrappers, the compiler cannot find mpi.mod because MPI_Fortran_INCLUDE_DIRS is not populated. * Use MPI::MPI_Fortran imported target instead of raw MPI variables Replace manual MPI_Fortran_LIBRARIES, MPI_Fortran_LINK_FLAGS, and MPI_Fortran_INCLUDE_DIRS usage with the MPI::MPI_Fortran imported target, which transitively carries all include dirs, compile flags, and link flags. This eliminates the CMAKE_Fortran_EXE_LINKER_FLAGS hack and the manual target_include_directories in H5PAR. * Update nvhpc version to 26.1 with CUDA version 13.1. (#6213) # branches: [develop] * Inherit Debug C build flags in Developer build mode (#6182) * Bump the github-actions group across 1 directory with 11 updates (#6215) * Bump the github-actions group across 1 directory with 11 updates Bumps the github-actions group with 11 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/cache](https://github.com/actions/cache) | `5.0.1` | `5.0.3` | | [lukka/get-cmake](https://github.com/lukka/get-cmake) | `4.2.1` | `4.2.3` | | [softwareforgood/check-artifact-v4-existence](https://github.com/softwareforgood/check-artifact-v4-existence) | `0.3.0` | `0.4.1` | | [github/codeql-action](https://github.com/github/codeql-action) | `3.31.9` | `4.32.2` | | [azure/trusted-signing-action](https://github.com/azure/trusted-signing-action) | `0.5.11` | `1.1.0` | | [cygwin/cygwin-install-action](https://github.com/cygwin/cygwin-install-action) | `7d2dc1e241644c3318bed9ec74115d1929baa681` | `2566376092c4e280f21131be027af3f5bb2420a4` | | [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials) | `5.1.1` | `6.0.0` | | [vmactions/freebsd-vm](https://github.com/vmactions/freebsd-vm) | `1.3.4` | `1.4.2` | | [vmactions/openbsd-vm](https://github.com/vmactions/openbsd-vm) | `1.3.1` | `1.3.5` | | [mpi4py/setup-mpi](https://github.com/mpi4py/setup-mpi) | `1.4.1` | `1.4.2` | | [actions/setup-python](https://github.com/actions/setup-python) | `6.1.0` | `6.2.0` | vmactions/openbsd-vm@d6c29ce1b4 (`1.3.5`) failed to run ssh on the github runner. 271a1ba62300483cfc58345ff9f425f1349a2cab for v1.3.4 was used instead. * Fix issue with some Subfiling VFD test files not getting deleted (#6212) * CMake: Fix Fortran cross-compilation support Refactor the cross-compilation infrastructure to rely on the standard CMAKE_CROSSCOMPILING_EMULATOR variable instead of the custom CROSSCOMPILING_PATH environment hack. Key changes: - Removed `ENVIRONMENT "${CROSSCOMPILING_PATH}"` from all test definitions. - Updated custom commands (e.g., H5match_types, H5_gen) to invoke the emulator explicitly when cross-compiling. - Updated ConfigureChecks.cmake and HDF5UseFortran.cmake to enable `try_run` checks when an emulator is defined. - Added config/toolchain/mingw-w64-x86-64-wine.sh wrapper to automatically locate MinGW runtime libraries (like libgfortran) for Wine execution. - Cleaned up toolchain files to remove hardcoded emulator paths, deferring configuration to the build environment. * Add Doxygen setup that results in missing Doygen documentation. (#6217) * Added setup-doxygen action in ctest.yml Ubuntu gcc workflow. * Also added actions/checkout for setup-doxygen. * Fixes link checker failure (#6219) Removed https:// as a workaround to avoid error by the link checker. * Remove force-setting of ZLIB_USE_EXTERNAL / SZIP_USE_EXTERNAL (#6222) Removes the force-setting of ZLIB_USE_EXTERNAL and SZIP_USE_EXTERNAL to ON when HDF5_ALLOW_EXTERNAL_SUPPORT is GIT or TGZ so that zlib and szip can be independently built from the system or externally as desired * Truncate Subfiling VFD's stub file when truncating subfiles (#6210) Ensure that the Subfiling VFD's stub file gets truncated when subfiles are being truncated to avoid a potentially unreadable file when the EOF doesn't match the stored EOF value Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Add CMake function to extract pkg-config info from libraries (#6220) * Consistent extension for C++ (#6214) Except for this file, all use cpp instead of cxx. No obvious reason why the same file types should have different extensions. * Enable Windows ARM64 CTest CI for release binaries (#6177) * ci: add Windows ARM64 MSVC CTest job * ci: add MSYS2 clangarm64 build on Windows ARM64 * cmake: add MSVC ARM64 presets for Windows * zlib: fix MSVC static library flags for ARM64 builds * Renamed .hxx file to .h and updated the #include for it. * Committing clang-format changes --------- Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julien Schueller <schueller@phimeca.com> Co-authored-by: Martin Diehl <mail@martin-diehl.net> Co-authored-by: Harish RS <harish.rajaselvan@multicorewareinc.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
318 lines
11 KiB
YAML
318 lines
11 KiB
YAML
name: Java Implementation Testing (FFM vs JNI)
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# Test both FFM and JNI implementations across multiple Java versions
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on:
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pull_request:
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branches: [ develop, main ]
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paths:
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- 'java/**'
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- 'CMakeBuildOptions.cmake'
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- 'CMakePresets.json'
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- 'config/cmake-presets/hidden-presets.json'
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- '.github/workflows/java-implementation-test.yml'
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- '.github/scripts/test-java-implementations.sh'
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workflow_call:
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inputs:
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java_versions:
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description: 'Java versions to test (comma-separated)'
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type: string
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required: false
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default: '11,17,21,24'
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test_mode:
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description: 'Test mode (build, maven, full)'
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type: string
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required: false
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default: 'build'
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platforms:
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description: 'Platforms to test'
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type: string
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required: false
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default: 'ubuntu-latest'
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workflow_dispatch:
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inputs:
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java_versions:
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description: 'Java versions to test'
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type: string
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required: false
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default: '11,17,21,24'
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test_mode:
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description: 'Test mode'
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type: choice
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required: false
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default: 'build'
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options:
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- 'build'
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- 'maven'
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- 'full'
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platforms:
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description: 'Platforms to test'
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type: choice
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required: false
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default: 'ubuntu-latest'
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options:
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- 'ubuntu-latest'
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- 'windows-latest'
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- 'macos-latest'
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- 'all-platforms'
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env:
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CMAKE_GENERATOR: Ninja
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jobs:
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setup-matrix:
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.generate-matrix.outputs.matrix }}
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steps:
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- name: Generate test matrix
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id: generate-matrix
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run: |
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# Parse inputs
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JAVA_VERSIONS="${{ inputs.java_versions || '11,17,21,25' }}"
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PLATFORMS="${{ inputs.platforms || 'ubuntu-latest' }}"
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# Expand platforms if needed
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if [[ "$PLATFORMS" == "all-platforms" ]]; then
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PLATFORMS="ubuntu-latest,windows-latest,macos-latest"
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fi
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# Generate matrix
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matrix_json="["
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first_entry=true
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for platform in $(echo "$PLATFORMS" | tr ',' ' '); do
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for java_version in $(echo "$JAVA_VERSIONS" | tr ',' ' '); do
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# Determine available implementations
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if [[ $java_version -ge 25 ]]; then
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implementations="ffm jni"
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else
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implementations="jni"
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fi
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for impl in $implementations; do
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if [ "$first_entry" = true ]; then
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first_entry=false
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else
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matrix_json="$matrix_json,"
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fi
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matrix_json="$matrix_json{\"os\":\"$platform\",\"java-version\":\"$java_version\",\"implementation\":\"$impl\"}"
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done
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done
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done
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matrix_json="$matrix_json]"
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echo "Generated matrix:"
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echo "$matrix_json" | jq '.'
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echo "matrix=$matrix_json" >> $GITHUB_OUTPUT
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test-implementations:
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needs: setup-matrix
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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include: ${{ fromJson(needs.setup-matrix.outputs.matrix) }}
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name: Test Java ${{ matrix.java-version }} ${{ matrix.implementation }} on ${{ matrix.os }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
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with:
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submodules: recursive
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- name: Set up Java ${{ matrix.java-version }} (${{ matrix.implementation }})
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uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
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with:
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distribution: ${{ matrix.implementation == 'ffm' && 'oracle' || 'temurin' }}
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java-version: ${{ matrix.implementation == 'ffm' && '25' || matrix.java-version }}
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- name: Setup jextract (FFM builds only)
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if: ${{ matrix.implementation == 'ffm' }}
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uses: ./.github/actions/setup-jextract
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with:
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java-version: '25'
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- name: Setup Build Environment (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get install -y ninja-build libaec-dev zlib1g-dev
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- name: Setup Build Environment (macOS)
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if: runner.os == 'macOS'
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run: |
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brew install ninja libaec
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- name: Setup Build Environment (Windows)
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if: runner.os == 'Windows'
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run: |
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choco install ninja
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- name: Cache CMake build
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uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v4
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with:
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path: |
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build-test-*
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key: ${{ runner.os }}-java${{ matrix.java-version }}-${{ matrix.implementation }}-${{ hashFiles('**/CMakeLists.txt', 'CMakePresets.json') }}
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restore-keys: |
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${{ runner.os }}-java${{ matrix.java-version }}-${{ matrix.implementation }}-
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${{ runner.os }}-java${{ matrix.java-version }}-
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- name: Verify Java version and implementation compatibility
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run: |
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java -version
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echo "Testing Java ${{ matrix.java-version }} with ${{ matrix.implementation }} implementation"
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# Additional validation for FFM
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if [[ "${{ matrix.implementation }}" == "ffm" ]]; then
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if [[ ${{ matrix.java-version }} -lt 25 ]]; then
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echo "::error::FFM implementation requires Java 25, got Java ${{ matrix.java-version }}"
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exit 1
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fi
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echo "FFM implementation validated for Java ${{ matrix.java-version }}"
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fi
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- name: Run implementation tests
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shell: bash
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run: |
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chmod +x .github/scripts/test-java-implementations.sh
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.github/scripts/test-java-implementations.sh \
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${{ matrix.java-version }} \
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${{ matrix.implementation }} \
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${{ inputs.test_mode || 'build' }}
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- name: Upload build artifacts on failure
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if: failure()
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uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v5
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with:
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name: build-logs-${{ matrix.os }}-java${{ matrix.java-version }}-${{ matrix.implementation }}
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path: |
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build-test-*/CMakeCache.txt
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build-test-*/CMakeFiles/CMakeError.log
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build-test-*/CMakeFiles/CMakeOutput.log
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retention-days: 7
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- name: Upload Maven artifacts (if generated)
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if: inputs.test_mode == 'maven' || inputs.test_mode == 'full'
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uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v5
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with:
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name: maven-artifacts-${{ matrix.os }}-java${{ matrix.java-version }}-${{ matrix.implementation }}
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path: |
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build-test-*/java/**/target/*.jar
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build-test-*/java/**/pom.xml
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retention-days: 3
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validate-artifacts:
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needs: [setup-matrix, test-implementations]
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runs-on: ubuntu-latest
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if: inputs.test_mode == 'maven' || inputs.test_mode == 'full'
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steps:
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- name: Checkout repository
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
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- name: Download all Maven artifacts
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uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
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with:
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pattern: maven-artifacts-*
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path: artifacts/
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- name: Validate artifact differentiation
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run: |
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echo "Validating Maven artifact differentiation..."
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# Check for FFM artifacts
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ffm_artifacts=$(find artifacts/ -name "*hdf5-java-ffm*" | wc -l)
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jni_artifacts=$(find artifacts/ -name "*hdf5-java-jni*" | wc -l)
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echo "Found $ffm_artifacts FFM artifacts and $jni_artifacts JNI artifacts"
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if [[ $ffm_artifacts -eq 0 && $jni_artifacts -eq 0 ]]; then
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echo "::error::No Maven artifacts found!"
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exit 1
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fi
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# Verify no mixed artifacts
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mixed_artifacts=$(find artifacts/ -name "*hdf5-java-*" | grep -v -E "(ffm|jni)" | wc -l)
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if [[ $mixed_artifacts -gt 0 ]]; then
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echo "::error::Found artifacts without proper FFM/JNI differentiation"
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find artifacts/ -name "*hdf5-java-*" | grep -v -E "(ffm|jni)"
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exit 1
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fi
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echo "✅ Artifact differentiation validation passed"
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- name: Validate POM files
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run: |
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echo "Validating POM file contents..."
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for pom in $(find artifacts/ -name "pom.xml"); do
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echo "Checking POM: $pom"
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# Extract artifact ID
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artifact_id=$(grep -o '<artifactId>hdf5-java-[^<]*</artifactId>' "$pom" | sed 's/<[^>]*>//g')
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echo "Artifact ID: $artifact_id"
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# Validate implementation metadata
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if grep -q "hdf5-java-ffm" "$pom"; then
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if ! grep -q "FFM" "$pom"; then
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echo "::error::FFM POM missing implementation metadata"
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exit 1
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fi
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echo "✅ FFM POM validation passed"
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elif grep -q "hdf5-java-jni" "$pom"; then
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if ! grep -q "JNI" "$pom"; then
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echo "::error::JNI POM missing implementation metadata"
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exit 1
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fi
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echo "✅ JNI POM validation passed"
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else
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echo "::error::POM has unrecognized artifact ID: $artifact_id"
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exit 1
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fi
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done
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report-results:
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needs: [setup-matrix, test-implementations, validate-artifacts]
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runs-on: ubuntu-latest
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if: always()
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steps:
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- name: Generate test report
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run: |
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echo "## Java Implementation Test Results" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "### Test Configuration" >> $GITHUB_STEP_SUMMARY
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echo "- **Java Versions**: ${{ inputs.java_versions || '11,17,21,25' }}" >> $GITHUB_STEP_SUMMARY
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echo "- **Test Mode**: ${{ inputs.test_mode || 'build' }}" >> $GITHUB_STEP_SUMMARY
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echo "- **Platforms**: ${{ inputs.platforms || 'ubuntu-latest' }}" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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# Report job statuses
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if [[ "${{ needs.test-implementations.result }}" == "success" ]]; then
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echo "✅ **Implementation Tests**: PASSED" >> $GITHUB_STEP_SUMMARY
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else
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echo "❌ **Implementation Tests**: FAILED" >> $GITHUB_STEP_SUMMARY
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fi
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if [[ "${{ needs.validate-artifacts.result }}" == "success" ]]; then
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echo "✅ **Artifact Validation**: PASSED" >> $GITHUB_STEP_SUMMARY
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elif [[ "${{ needs.validate-artifacts.result }}" == "skipped" ]]; then
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echo "⏭️ **Artifact Validation**: SKIPPED" >> $GITHUB_STEP_SUMMARY
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else
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echo "❌ **Artifact Validation**: FAILED" >> $GITHUB_STEP_SUMMARY
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fi
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "### Implementation Matrix" >> $GITHUB_STEP_SUMMARY
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echo "| Java Version | FFM Support | JNI Support |" >> $GITHUB_STEP_SUMMARY
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echo "|--------------|-------------|-------------|" >> $GITHUB_STEP_SUMMARY
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echo "| 11 | ❌ | ✅ |" >> $GITHUB_STEP_SUMMARY
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echo "| 17 | ❌ | ✅ |" >> $GITHUB_STEP_SUMMARY
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echo "| 21 | ❌ | ✅ |" >> $GITHUB_STEP_SUMMARY
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echo "| 24+ | ✅ (optional) | ✅ (default) |" >> $GITHUB_STEP_SUMMARY |